SIMPULAN DAN SARAN Identifikasi Protein-Protein Signifikan Yang Berasosiasi Dengan Diabetes Mellitus (Dm) Tipe 2 Menggunakan Analisis Topologi Jejaring Protein-Protein Interaction

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1. Lampiran source code konstruksi jejaring PPI, subnetwork, analisis

topologi dan konstruksi jejaring penyangga import networkx as nx import xlwt as xl nama fungsi : gabung_2_fppils_nm_file 7an : menggabung dua file PPI input : list nama file PPI dan nama file PPI gabungan output : --- def gabung_2_fppils_nm_file: ff = openls_nm_file[2],w for i in range0,lenls_nm_file-1: f = openls_nm_file[i] ln = f.readline while ln: ff.writeln ln = f.readline f.close ff.close nama fungsi : fProt_to_lsProtnm_fprot 7an : memindahkan seed protein dari file -- list seed protein list pasangan biner protein input : nama file seed protein output : list prot lsProt : [p1, p2, p3, ..., pn] def fProt_to_lsProtnm_fprot: f = opennm_fprot listProt = [] sprot = f.readline membaca line pertama dalam file while sprot: sprot = sprot.replace\n, listProt = listProt + [sprot] sprot = f.readline membaca line berikutnya dalam file return listProt nama fungsi : lsProt_to_lsBProtlsProt 7an : membentuk pasangan biner protein dari list protein input : list protein lsProt output : list pasangan biner prot lsBProt: [p1,p2,p1,p3,...,p1,pn,...,p5,p6,p5,p7,...,p5,pn,...,pn- 1,pn] def lsProt_to_lsBProtlsProt: listBProt = [] temp = ; for i in range0,lenlsProt: temp = lsProt[i] for j in rangei+1, lenlsProt: listBProt = listBProt + [temp,lsProt[j]] return listBProt nama fungsi : fPPI_to_lsPPInm_fppi 7an : memindahkan file interaksi biner protein yg diperoleh dari STRING.db atau HPRD -- list interaksi biner antar protein input : nama file ppi output : list PPI lsPPI : [a,b,b,d,...,y,z] peruntukan output : lsPPI : digunakan untuk membangun jejaring PPI def fPPI_to_lsPPInm_fppi: f = opennm_fppi fileOk = True listPPI = [] list interaksi biner antar protein bppi = f.readline membaca line pertama interaksi biner protein ppi dlm file while bppi: bppi = bppi.replace\n, p = p1 = p2 = p: protein, p1: protein1, p2: protein2 for i in range0,lenbppi: ch = bppi[i] if ch = \t: p = p + ch if ch == \t: p1 = temp = p p = if i == lenbppi-1: p2 = temp = p p = p1 = p1.replace-, p1 = p1.replace , p2 = p2.replace-, p2 = p2.replace , if p1 = p2 and notp1,p2 in listPPI and notp2,p1 in listPPI and p1= and p2= : listPPI = listPPI + [p1,p2] else: fileOk = False bppi = f.readline f.close if not fileOk: f = opennm_fppi,w for i in range0,lenlistPPI: dt = listPPI[i] f.writedt[0]+\t+dt[1]+\n f.close return listPPI def del_Dupl_PPIlsPPI,lsBC005: listPPI = [] for i in range0,lenlsPPI: p1 = lsPPI[i][0] p2 = lsPPI[i][1] if p1 in lsBC005 and p2 in lsBC005 and p1 = p2 and notp1,p2 in listPPI and notp2,p1 in listPPI and p1= and p2= : listPPI = listPPI + [p1,p2] return listPPI nama fungsi : empty_graph 7an : menciptakan sebuah graph G yang masih kosong input : --- output : sebuah graph G kosong 29 def empty_graph: return nx.Graph nama fungsi : const_networkdtlsPPI 7an : menciptakan graph G kemudian membangun network G PPI dari sebuah list PPI : [p1,p7,p3,p6,p10,p22,...] input : sebuah list PPI : dtlsPPI : [p1,p7,p3,p6,p10,p22,...] output : sebuah network graph PPI : G peruntukan output : G PPI: untuk dilakukan analisis topologi def const_networklsPPI: menciptakan empty graph G G = empty_graph konstruksi network PPI dari sebuah list PPI [p1,p7,p3,p6,p10,p22,...] G.add_edges_fromlsPPI return G nama fungsi : get_allshortespathG, lsBProtAsal, tipe 7an : mencari semua jalur terpendek dari pasangan biner protein asal input : G: sebuah network yang terbentuk dari list PPI lsBProtAsal: list pasangan biner protein asal tipe == 1: mencari semua shortest_path default networkx tipe == 2: mencari semua shortest_path dengan algoritme dijstra tipe == 3: mencari semua shortest_path berdasarkan akumalasi nilai degree terbesar dari semua alternatif jalur yang ditemukan untuk tiap pasangan biner protein asal output : list shortest_path dari semua pasangan biner protein asal peruntukan output : untuk membangun subnetwork PPI dari network PPI def get_allshortespathG, lsBProtAsal, tipe, lspBC005: lsShortestPath = [] ok = True lsBSeedProtEmpty = [] jmlBSeedProt = 0 jmlAllSP = 0 jmlSP = 0 if tipe == 1: menemukan 1 jalur terpendek tiap pasang protein for i in range0,lenlsBProtAsal: bpa = lsBProtAsal[i] biner protein asal try: tempshortest_path = nx.shortest_pathG,bpa[0],bpa[1] lsShortestPath = lsShortestPath + [tempshortest_path] except: lsShortestPath = lsShortestPath + [] elif tipe == 2: menemukan 1 jalur terpendek dengan metode dijkstar tiap pasang protein for i in range0,lenlsBProtAsal: bpa = lsBProtAsal[i] biner protein asal try: tempshortest_path = nx.dijkstra_pathG,bpa[0],bpa[1] lsShortestPath = lsShortestPath + [tempshortest_path] except: lsShortestPath = lsShortestPath + [] elif tipe == 3: menemukan beberapa jalur terpendek tiap pasang protein